Biochemistry Exam 3 – Sapling

Identify the key structural features of a DNA molecule.

1. The backbone of DNA is made of a sugar and a phosphate molecule. 2. DNA bases are always paired using Watson-Crick base pairing. 3. DNA strands are antiparallel and include a 5′ end and a 3′ end.

Identify the statements that describe the structure of DNA.

1. The five-carbon sugar of DNA is called deoxyribose. 2. A DNA double helix contains two sugar-phosphate backbones oriented in opposite directions. 3. Adenine is paired with thymine, and guanine is paired with cytosine.

There are two types of nucleic acids, DNA and RNA. Nearly all organisms use DNA, not RNA, as the central repository for genetic information. Choose the statements that explain this phenomenon.

1. DNA has a double-stranded structure that ensures an accurate mechanism of duplication. 2. DNA is more resistant against enzymes that degrade nucleic acids. 3. DNA is more stable than RNA.

What evidence supports the hypothesis that RNA was the genetic material early in evolutionary history?

1. Some viruses have RNA genomes. 2. RNA can catalyze enzymatic reactions.

Which of the following statements describes purines and pyrimidines in DNA molecules?

1. Purines consist of a two-ring structure. 2. Purines form hydrogen bonds with pyrimidines.

Classify each description as an example of the primary, secondary, or higher-order structure of DNA.

Primary Structure: 1. the sequence of nucleotides 2. any base sequence Secondary Structure: 1. Adenine forms hydrogen bonds with thymine 2. Hydrogen bonds between complementary base pair results in a double helix. Higher-Order Structure: 1. Double helix coiling around proteins known as histones. 2. Tightly coiling nucleosomes that forms chromosomes.

DNA Packaging

1. The less condensed form of chromatin is euchromatin. 2. The inactive form of chromatin is heterochromatin. 3. A core composed of eight histone proteins interacts with DNA through hydrogen bonding and ionic bonds. 4. If DNA is described as beads on a string, then the bead is a nucleosome. 5. The more darkly stained form of chromatin is heterochromatin. 6. If DNA is described as beads on a string, then the string is the DNA molecule. 7. A nuclesome is a DNA protein complex.

Classify each feature as describing prokaryotic DNA structure or eukaryotic DNA structure.

Prokaryotic 1. Condensed only by DNA supercoiling 2. DNA is circular 3. Does not have a telomere region. 4. Occurs as a single looped structure. Eukaryotic 1. Condensed around histone proteins. 2. DNA is linear. 3. Has a repeating telomere region. 4. Occurs as multiple chromosomes.

Genes, Alleles, and Chromosomes

Gene 1. A short segment of a chromosome that codes for an RNA molecule. 2. A functional unit of heredity. Allele 1. An alternative form of a particular gene. Chromosome 1. long DNA molecules visible during mitosis 2. large genetic element that carries genes essential to cellular function

What transformation occurs during each of the following processes?

Translation: RNA > Protein Transcription: DNA > RNA Reverse Transcription: RNA > DNA Replication: DNA > DNA

Sort each phrase or term as relating to replication, transcription, or translation.

Replication 1. Both DNA strands are duplicated. 2. Described as semi-conservative. 3. DNA Polymerase Transcription 1. Single DNA strand is used to produce mRNA. Translation 1. Amino acids added to peptide chain. 2. Requires tRNA 3. Ribosome

How does the structure of DNA encode genetic information?

the sequence of bases

Since DNA is replicated semiconservatively, what does each new daughter cell receive from the parent cell after replication and mitosis?

One of the original strands and one new strand

Match each protein to its role in DNA replication.

1. DNA topoisomerase relaxes the supercoiled DNA. 2. Helicase unwinds the DNA double helix. 3. SSB proteins prevent the reannealing of DNA strands. 4. DNA polymerase III synthesizes new DNA. 5. DNA Ligase connects the separated DNA segments.

Enzymes that play a role in eukaryotic DNA replication are listed below. Match the enzyme names with their functions.

1. Helicases use energy from ATP hydrolysis to unwind nucleic acid duplexes. 2. DNA polymerases may proofread newly sythesized DNA. 3. DNA ligases join discontinuous DNA segments. During DNA replication, this produces a continuous lagging strand. 4. Ribonucleases degrade RNA, excising the RNA primer during DNA replication. 5. DNA polymerases extend pre-existing deoxyribonucleotide chains. 6. Primases synthesizes short RNA segments, which then can be extended during DNA replication.

Arrange the steps of DNA replication in the order that they occur.

Helicases unwinds the DNA double helix. Single stranded DNA-binding proteins bind to each template strand. RNA primers are added. DNA polymerase synthesizes DNA. RNA primers are removed. DNA ligase joins DNA segments together.

Which of the following statements regarding DNA replication are true?

1. Replication usually takes place in the 5′ to 3′ direction. 2. Eukaryotic chromosomes have more than one origin of replication.

Why do cells maintain low fidelity, error prone DNA polymerases for certain tasks when more accurate, high fidelity DNA polymerases are available?

Distortions in the DNA template strand stall synthesis by high fidelity polymerases and recruiting low fidelity polymerases allows replication to continue.

According to the central dogma, double-stranded DNA serves as the template for the production of RNA during transcription. Which of the two DNA strands serves as the template for transcription?

Either DNA strand may be used as a template by RNA polymerase, but a single DNA strand oriented in the 3′-5′ direction is used as a template each time transcription occurs.

Match each description to a phase of transcription in humans.

Initiation: 1. Transcription factors and RNA polymerase bind the gene promoter. 2. The DNA double helix unwinds, and RNA synthesis begins. Elongation: 1. RNA polymerase reads the template strand and synthesizes RNA in the 5′ to 3′ direction. 2. The newly transcribed RNA transcript is proofread for errors. Termination: 1. The RNA strand is cleaved and released from the transcription complex. 2. The DNA polymerase detaches from the DNA. 3. The RNA polymerase stops adding base pairs when it reaches a certain DNA sequence that signals the end of the gene.

Place the steps of eukaryotic transcription in order of occurrence.

1. RNA polymerase unwinds DNA. 2. Ribonucleotides align complementary DNA nucleotides. 3. RNA polymerase links tri-phosphate ribonucleotides together. 4. Guanylyl Transferase adds a guanine cap to the 5′ end of the mRNA. 5. RNA polymerase is released from the DNA. 6. Splicing and Polyadenylation events modify the mRNA.

What is the role of the eukaryotic promoter in transcription?

the site where transcription factors bind and function

Identify the statements that are features of a promoter.

1. In prokaryotes, the promoter contains a -35 and -10 region upstream of the transcription start site. 2. In both prokaryotes and eukaryotes, the promoter is located in the 5\’ direction, upstream from the transcription start site. 3. In eukaryotes, the promoter recruits the preinitiation complex, which includes the TATA-binding protein.

What is a transcription factor?

a protein that binds to a specific DNA sequence to regulate transcription

What happens during the initiation step of DNA transcription?

A portion of the DNA unwinds and RNA polymerase attaches to the DNA within the transcription bubble.

What happens during the elongation step of DNA transcription?

RNA polymerase moves along the template strand of the DNA creating an mRNA strand.

What happens during the termination step of DNA transcription?

The mRNA detaches from the RNA polymerase as the RNA polymerase leaves the DNA strand.

Put the following steps of eukaryotic transcription elongation in order starting with the shift from transcription initiation, and ending with termination.

1. The C-Terminal domain of RNA polymerase is phosphorylated, causing a conformational change in the complex. 2. Polymerase releases many general transcription factors. 3. An elongation protein complex binds to the phosphorylated C-Terminal domain. 4. The 3′ hydroxyl group of the growing RNA chain attacks the alpha phosphate of the incoming ribonucleoside triphosphate. 5. RNA polymerase is released and dephosphorylated.

In what order would the RNA polymerase encounter the following elements in the DNA sequence of the gene?

1. Transcription Start Site 2. 5′ UTR 3. Translation Initiation Codon 4. Splice Donor Site 5. Translation Termination Codon 6. 3′ UTR

Complete the sentences by moving the terms to the appropriate sentences. Choose the best, or most specific, term for each sentence.

1. An intron is a segment of a gene that does not code for a product. 2. An open reading frame is a DNA sequence that begins with a start codon and ends with a stop codon. 3. A gene is a DNA segment that is transcribed and processed to produce a specific protein or RNA product. 4. An expressed sequence tag is a small cDNA sequence, synthesized from mRNA and sequenced, that can be used to identify a particular gene. 5. An operon contains genes for related proteins and regions that function in gene transcription.

Transcription vs. Translation

Transcription: 1. takes place in the nucleus 2. builds strands of mRNA Translation: 1. takes place in the ribosomes 2. produces a protein 3. involves tRNA

Match each cellular component to a role in transcription or translation in eukaryotic cells.

1. RNA polymerase adds RNA nucleotides to a growing RNA using a DNA template. 2. Nucleus contains DNA in the cell. 3. Promoter is the region of DNA that recruits the transcriptional machinery 4. tRNA provides amino acids to the growing protein chain. 5. Ribosome is the site of protein synthesis

How does the process of translation in prokaryotes differ from translation in eukaryotes?

Prokaryotic Translation 1. Translation can begin as soon as the 5′ end of the mRNA is free of the DNA. 2. Only free floating ribosomes in the cytoplasm are involved. 3. The entire RNA transcript is used without any modifcations. Eukaryotic Translation 1. Introns are removed from pre-mRNA before ribosomes can use the mRNA. 2. Mature mRNA has a cap on one end and a poly-A tail on the other end. 3. Ribosomes are located both in the cytoplasm and attached to the endoplasmic reticulum.

Every ribosome has three tRNA binding sites: the A site, the P site, and the E site. Which sites do which?

1. The P site binds the tRNA molecule that is attached to the growing peptide chain. 2. The site that binds the aminoacyl-tRNA is the A site. 3. The E site may be bound to uncharged tRNA. 4. The site that binds the peptidyl-tRNA is the P site.

What is the order of protein synthesis?

1. The smaller subunit of the ribosome attaches to the mRNA strand and moves along it. 2. A codon on the mRNA strand binds with a complementary anticodon on a tRNA molecule carrying an amino acid. 3. New amino acids are added to the polypeptide chain by the ribosome. 4. Once the amino acids have been removed from the tRNA molecules, the tRNA’s leave the ribosome.

Which of the following events occur during eukaryotic translation initiation?

The small ribosomal subunit binds with a specific tRNA to the mRNA and scans for a start codon.

Which of the following events occur during eukaryotic translation elongation?

A tRNA binds a codon and the ribosome adds amino acids from each tRNA to the polypeptide chain.

Which of the following events occur during eukaryotic translation termination?

A protein recognizes the stop codon and the ribosome dissociates from the mRNA.

What is a codon?

a sequence of three nucleotides encoding a specific amino acid

An anticodon is a sequence of three nucleotides that

is found on transfer RNA and is complementary to messenger RNA codons.

Which mRNA codon functions as the start codon, directing the ribosome to begin translating the mRNA from the correct end?

AUG

How do stop codons on mRNA function to end protein synthesis?

A stop codon does not code for an amino acid, so protein synthesis ends when no new amino acid is added to the polypeptide chain.

What strategies do cells use to ensure that newly replicated DNA does not contain errors?

1. Enzymes proofread the DNA after the DNA has been replicated and replace any mismatched nucleotides. 2. As DNA polymerase synthesizes new DNA, the DNA polymerase finds and corrects misplaced nucleotides. 3. Enzymes find misshapen DNA sequences prior to replication and remove and resynthesize those sequences.

What generally causes thymine dimers to form in a strand of DNA, and why are thymine dimers a problem?

Thymine dimers, which can be produced by ultraviolet radiation, can lead to cancer-causing mutations.

Classify the statements as describing either a substituion mutation or a frameshift mutation.

Substitution 1. This mutation can only affect a single amino acid upon translation. 2. A single nucleotide is switched for another in the template DNA strand. Frameshift 1. Multiple nucleotides are added or removed from the template DNA strand. 2. This mutation can cause the insertion or deletion of a amino acid.

Classify the statements as describing either point, insertion, or deletion mutations.

Point 1. The base sequence GTA becomes TTA. 2. A single nucleotide is switched for another in the template DNA strand. Insertion 1. Multiple nucleotides are added to the template DNA strand. 2. The base sequence CTA becomes CTTAG. 3. This mutation can cause the insertion of an amino acid. Deletion 1. The base sequence CTTAG becomes CTA. 2. Multiple nucleotides are removed from the template DNA strand.

Determine whether each of the following mutations is a silent mutation, missense mutation, or nonsense mutation.

Silent Mutation: 1. A base substitution does not have any notable effects. Missense Mutation: 1. Protein is of normal length but altered function. Nonsense Protein: 1. Protein is shortened, unfunctional protein

Match each term below to a definition.

1. A mutation that results in reduced or absent protein function (Loss of function mutation) 2. A mutation that is only expressed in a certain situation. (Conditional Mutation) 3. A mutation within the same gene that masks another mutation. (Intragenic Suppressor Mutation) 4. A mutation that results in a new or additional protein function (Gain of function mutation) 5. A mutation in a separate gene that masks another mutation. (Intergenic Suppressor Mutation)

Classify each of the characteristics below as pertaining to a gene or a genome.

Gene 1. Nucleotide sequence that can encode a protein 2. Humans have approximately 21000 3. Is thousands of base pairs long. Genome 1. Is the collection of genetic information in a cell 2. Defines humans as a species 3. Is millions of base pairs long

How are protein-coding genes identified from eukaryotic DNA sequences?

1. looking for partial complementarity between expressed mRNAs and genomic DNA 2. identifying sequence features commonly found near genes using computational analysis

What is proteomics?

the study of the collection of proteins found within a cell, tissue, or organism

How is it possible that humans have so few genes but can generate so many proteins?

alternative splicing of mRNAs produced from one gene generates different proteins

Which description is the best definition of recombinant DNA?

DNA that is composed of a combination of DNA sequences from two or more organisms.

Describe the contruction of a recombinant plasmid containing the gene for the green fluorescent protein (GFP) and the insertion of the plasmid into a bacterial cell by placing the steps in order.

1. Use PCR to amplify the gene for GFP. 2. Preform a restriction digestion of the GFP gene and the plasmid. 3. Ligate together the GFP gene and the plasmid to generate a recombinant plasmid. 4. Transform bacteria with the recombinant plasmid using electroporation. 5. Plate the bacterial cells, and screen for positive transformants.

Plasmids are small circular DNA molecules found in bacteria that replicate separately from chromosomes. Why are plasmids essential for recombinant DNA technology?

DNA from a gene of interest can be inserted into a plasmid, then the modified plasmid can be inserted into a bacterial cell to make many copies of a gene of interest.

What is complementary DNA (cDNA)?

a double-stranded DNA molecule that is a copy of an mRNA

HIV is a retrovirus. How are retroviruses unique from other types of viruses?

They use reverse transcriptase to make DNA from RNA.

Complementary DNA (cDNA) is a double-stranded molecule. In the laboratory, how is cDNA generated from a eukaryotic messenger RNA (mRNA)?

Reverse transcriptase generates a single-stranded cDNA and then DNA polymerase synthesizes the complementary strand.

What is the purpose of the polymerase chain reaction (PCR)?

generate copies of a piece of DNA

What reagents are needed for a typical polymerase chain reaction (PCR)?

1. Four nucloetides (A, T, C, G) 2. Taq polymerase 3. Two primers 4. Template DNA

Why is Taq polymerase used as the DNA polymerase in the polymerase chain reaction (PCR)?

It is thermodynamically stable at the temperature used to separate the DNA strands.

In the polymerase chain reaction (PCR), early replication errors affect a larger percentage of PCR products than late replication errors.

Less DNA in early cycles results in a higher overall proportion of copies containing the error because each round uses the fragment from earlier rounds as templates.

What is a restriction enzyme?

enzymes that can cleave DNA molecules at or near a specific nucleotide sequence

How are DNA fragments separated using gel electrophoresis?

Larger DNA fragments move more slowly through the gel than do smaller fragments.

How do scientists confirm that a cell has incorporated recombinant DNA?

1. perform polymerase chain reaction and run a gel 2. grow cells in the presence of an antibiotic 3. screen for the expression of a reporter gene

Which of the following describes sequencing?

determining the order of nucleotides in a DNA molecule

Order the steps required to sequence a region of DNA using dideoxy sequencing.

1. Add a primer, deoxynucleotides, dideoxynucleotides, and DNA polymerase 2. Denature the double stranded DNA. 3. A primer binds to the single stranded DNA template. 4. DNA polymerase extends the primer, incorporating deoxynucleotides. 5. A labeled, dideooxynucleotide terminates the growing DNA chain. 6. Capillary Electrophoresis separates the mixture of DNA fragments by size.